The RiboNets project lies at the interface of computer science and synthetic biology. The project aims at programming cellular networks and community behavior using newly engineered RNA based devices (RNAdevs) that transmit and process information within cells. We kicked off in September 2013 and the consortium will work the next three years on that exciting research topic,

RNAdevs can be seen as small molecular modules that regulate gene expression and function mainly based on ribonucleic acid sequences. Naturally occurring examples are so called riboswitches or sRNA-mRNA pairs. Revealing the actual regulatory mechanism which is hidden behind the naturally occurring elements is a tedious and time consuming task. Furthermore most of these elements are building blocks of a higher order regulatory network. To overcome these limitations we aim to newly design RNAdevs of which the regulation mechanism is engineered at the beginning and subsequently experimentally verified.

missionWe want to develop a newly designed toolbox for cellular computing which will be created following a three-step process: i) rational design and analysis of RNA-based devices using computer based approaches, ii) selecting best performers in vitro within highly parallel microfluidic reactors, and iii) integrating and testing them in living cells.

Having a compiled toolbox that contains well characterized, synthetic RNAdevs with efficient regulation, we plan to connect them to more complex networks and use them for instance to reprogram of community behavior.

Our multi-disciplinary approach blends the three layers of in silico, in vitro and in vivo analysis and will foster the successful engineering of functional RNAdevs and higher order RNA circuits. During the project, generic computational models, efficient software tools for the design of RNA based devices as well as experimental protocols will be developed and released to the scientific community. This will enable other groups in the emerging fields of Synthetic Biology and Natural Computing to build upon our findings and to speed up their research processes towards innovative solutions.




  • Our software tool, RNAblueprint, to fairly sample nucleic acid sequences compatible with multiple structural and sequence constraints is available here on github. Furthermore a python module to design RNA molecules using RNAblueprint, ViennaRNA and the NUPCK package can be found here.
  • Our RNAdevices database summarizing published designs is available. It is currently resticted to purely RNA based designs.
  • ODE systems implementing essential cellular process, i.e. transcription, translation and degradation, to model RNA based switches are available here on github.

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